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- PDB-5n1t: Crystal structure of complex between flavocytochrome c and copper... -

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Basic information

Entry
Database: PDB / ID: 5n1t
TitleCrystal structure of complex between flavocytochrome c and copper chaperone CopC from T. paradoxus
Components
  • CopC
  • Cytochrome C
  • flavin-binding subunit of sulfide dehydrogenase
KeywordsOXIDOREDUCTASE / COPPER CHAPERONE / SULFIDE REDUCTASE / PERIPLASM / PROTEIN COMPLEX
Function / homology
Function and homology information


response to copper ion / flavin adenine dinucleotide binding / periplasmic space / oxidoreductase activity / electron transfer activity / copper ion binding / heme binding / metal ion binding
Similarity search - Function
Flavocytochrome C Sulfide Dehydrogenase; Chain A Domain 3 / Flavocytochrome c sulphide dehydrogenase, flavin-binding domain / Flavocytochrome c sulphide dehydrogenase, flavin-binding / Flavocytochrome c sulphide dehydrogenase, flavin-binding domain superfamily / Flavocytochrome c sulphide dehydrogenase, flavin-binding / CopC domain / CopC domain / Copper resistance protein CopC/internalin, immunoglobulin-like / FAD/NAD-linked reductase, dimerisation domain superfamily / Cytochrome c ...Flavocytochrome C Sulfide Dehydrogenase; Chain A Domain 3 / Flavocytochrome c sulphide dehydrogenase, flavin-binding domain / Flavocytochrome c sulphide dehydrogenase, flavin-binding / Flavocytochrome c sulphide dehydrogenase, flavin-binding domain superfamily / Flavocytochrome c sulphide dehydrogenase, flavin-binding / CopC domain / CopC domain / Copper resistance protein CopC/internalin, immunoglobulin-like / FAD/NAD-linked reductase, dimerisation domain superfamily / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Immunoglobulin E-set / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / FLAVIN-ADENINE DINUCLEOTIDE / HEME C / Cytochrome C / Cytochrome C / CopC domain-containing protein
Similarity search - Component
Biological speciesThioalkalivibrio paradoxus ARh 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsOsipov, E.M. / Lilina, A.V. / Tikhonova, T.V. / Tsallagov, S.I. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
RNF14-24-00172 Russian Federation
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Structure of the flavocytochrome c sulfide dehydrogenase associated with the copper-binding protein CopC from the haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio paradoxusARh 1.
Authors: Osipov, E.M. / Lilina, A.V. / Tsallagov, S.I. / Safonova, T.N. / Sorokin, D.Y. / Tikhonova, T.V. / Popov, V.O.
History
DepositionFeb 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 14, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: flavin-binding subunit of sulfide dehydrogenase
B: Cytochrome C
M: CopC
W: CopC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3258
Polymers90,7654
Non-polymers1,5604
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-62 kcal/mol
Surface area27260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.530, 138.400, 155.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 4 molecules ABMW

#1: Protein flavin-binding subunit of sulfide dehydrogenase / Cytochrome C


Mass: 46264.730 Da / Num. of mol.: 1 / Mutation: C199CSS / Source method: isolated from a natural source
Source: (natural) Thioalkalivibrio paradoxus ARh 1 (bacteria)
References: UniProt: W0DP88
#2: Protein Cytochrome C


Mass: 10628.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thioalkalivibrio paradoxus ARh 1 (bacteria)
References: UniProt: W0DKT4
#3: Protein CopC / Copper chaperone CopC


Mass: 16935.814 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thioalkalivibrio paradoxus ARh 1 (bacteria)
References: UniProt: W0DSL1

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Non-polymers , 5 types, 61 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976256 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976256 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 28526 / % possible obs: 93.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 56 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.117 / Net I/σ(I): 9.8
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2841 / CC1/2: 0.79 / Rrim(I) all: 0.91 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FCD

1fcd


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.921 / SU B: 12.985 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 0.58 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25703 1385 5.1 %RANDOM
Rwork0.18593 ---
obs0.18949 25820 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.429 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--3.57 Å2-0 Å2
3----4.07 Å2
Refinement stepCycle: 1 / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5310 0 103 57 5470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195561
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9471.9617601
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1215710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64323.305233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.88115752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.571535
X-RAY DIFFRACTIONr_chiral_restr0.1170.2847
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214307
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.395.652858
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.5498.4583562
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7195.6522703
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.17474.6878177
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 103 -
Rwork0.32 1884 -
obs--99.75 %

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